Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China.
The New Zealand Institute for Plant and Food Research Limited, Auckland, 1025, New Zealand.
BMC Genomics. 2018 Nov 21;19(1):833. doi: 10.1186/s12864-018-5224-6.
Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the European (Pyrus communis) and Chinese (P. bretschneideri) pear genomes have not been published in public databases so far.
To anchor the scaffolds of P. bretschneideri 'DangshanSuli' (DS) v1.0 genome into pseudo-chromosomes, two genetic maps (MH and YM maps) were constructed using half sibling populations of Chinese pear crosses, 'Mantianhong' (MTH) × 'Hongxiangsu' (HXS) and 'Yuluxiang' (YLX) × MTH, from 345 and 162 seedlings, respectively, which were prepared for SNP discovery using genotyping-by-sequencing (GBS) technology. The MH and YM maps, each with 17 linkage groups (LGs), were constructed from 2606 and 2489 SNP markers and spanned 1847 and 1668 cM, respectively, with average marker intervals of 0.7. The two maps were further merged with a previously published genetic map (BD) based on the cross 'Bayuehong' (BYH) × 'Dangshansuli' (DS) to build a new integrated MH-YM-BD map. By using 7757 markers located on the integrated MH-YM-BD map, 898 scaffolds (400.57 Mb) of the DS v1.0 assembly were successfully anchored into 17 pseudo-chromosomes, accounting for 78.8% of the assembled genome size. About 88.31% of them (793 scaffolds) were directionally anchored with two or more markers on the pseudo-chromosomes. Furthermore, the errors in each pseudo-chromosome (especially 1, 5, 7 and 11) were manually corrected and pseudo-chromosomes 1, 5 and 7 were extended by adding 19, 12 and 14 scaffolds respectively in the newly constructed DS v1.1 genome. Synteny analyses revealed that the DS v1.1 genome had high collinearity with the apple genome, and the homologous fragments between pseudo-chromosomes were similar to those found in previous studies. Moreover, the red-skin trait of Asian pear was mapped to an identical locus as identified previously.
The accuracy of DS v1.1 genome was improved by using larger mapping populations and merged genetic map. With more than 400 MB anchored to 17 pseudo-chromosomes, the new DS v1.1 genome provides a critical tool that is essential for studies of pear genetics, genomics and molecular breeding.
染色体水平的参考基因组为全基因组关联研究（GWAS）和全基因组选择等基因组学研究提供了重要基础。到目前为止，欧洲梨（Pyrus communis）和中国梨（P. bretschneideri）的染色体水平序列尚未在公共数据库中公布。
为了将 P. bretschneideri 'DangshanSuli' (DS) v1.0 基因组的支架锚定到假染色体上，使用中国梨杂交群体 'Mantianhong' (MTH) × 'Hongxiangsu' (HXS) 和 'Yuluxiang' (YLX) × MTH 的半同胞群体构建了两个遗传图谱（MH 和 YM 图谱），分别从 345 和 162 个幼苗中获得，这些幼苗是使用基于测序的基因型 (GBS) 技术准备进行 SNP 发现的。MH 和 YM 图谱，每个图谱都有 17 个连锁群（LG），分别由 2606 和 2489 个 SNP 标记构建，分别覆盖 1847 和 1668cM，平均标记间隔为 0.7。这两个图谱进一步与之前基于 'Bayuehong' (BYH) × 'Dangshansuli' (DS) 杂交的遗传图谱 (BD) 融合，构建了一个新的综合 MH-YM-BD 图谱。利用位于综合 MH-YM-BD 图谱上的 7757 个标记，成功地将 898 个 DS v1.0 组装的支架（400.57Mb）锚定到 17 个假染色体上，占组装基因组大小的 78.8%。其中约 88.31%（793 个支架）在假染色体上用两个或更多标记进行了定向锚定。此外，每个假染色体（特别是 1、5、7 和 11）中的错误都手动纠正，并且在新构建的 DS v1.1 基因组中分别通过添加 19、12 和 14 个支架分别扩展了假染色体 1、5 和 7。同线性分析表明，DS v1.1 基因组与苹果基因组具有高度的共线性，并且假染色体之间的同源片段与之前的研究相似。此外，亚洲梨的红皮性状被映射到与之前相同的位置。
使用更大的图谱群体和合并的遗传图谱提高了 DS v1.1 基因组的准确性。通过将超过 400MB 锚定到 17 个假染色体上，新的 DS v1.1 基因组为梨遗传学、基因组学和分子育种研究提供了一个关键工具。
